Compare the lola motif distribution among promoter of all genes to the that of the opening set genes and lola bound genes
Project:
Author: Vivek
Generated: Wed Jan 19 2022, 07:10 AM
## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
## - in 'x': chrM, chrX_DS484099v1_random, chrX_DS484216v1_random, chrY_DS485329v1_random
## - in 'y': chrUn_DS483562v1, chrUn_DS484160v1, chrUn_DS484280v1, chrX_DS484953v1_random
## Make sure to always combine/compare objects based on the same reference
## genome (use suppressWarnings() to suppress this warning).
Look at the MNase profile at Lola target genes
Project: Promoter Opening
Author: Vivek
Generated: Wed Jan 19 2022, 07:11 AM
## There are 364 positive granges and 372 negative granges
## There are 364 positive granges and 372 negative granges
## There are 364 positive granges and 372 negative granges
## There are 364 positive granges and 372 negative granges
## There are 364 positive granges and 372 negative granges
## There are 364 positive granges and 372 negative granges
## R version 3.6.1 (2019-07-05)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
##
## locale:
## [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
## [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
## [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] pander_0.6.3 scales_1.0.0
## [3] matrixStats_0.55.0 cowplot_1.0.0
## [5] magrittr_1.5 tidyr_1.0.0
## [7] dplyr_0.8.3 reshape2_1.4.3
## [9] ggplot2_3.2.1 lattice_0.20-38
## [11] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.52.0
## [13] rtracklayer_1.44.4 Biostrings_2.52.0
## [15] XVector_0.24.0 GenomicRanges_1.36.1
## [17] GenomeInfoDb_1.20.0 IRanges_2.18.2
## [19] S4Vectors_0.22.1 BiocGenerics_0.30.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.5 Rsamtools_2.0.0
## [3] assertthat_0.2.1 zeallot_0.1.0
## [5] digest_0.6.20 R6_2.4.0
## [7] plyr_1.8.4 backports_1.1.4
## [9] evaluate_0.14 pillar_1.4.2
## [11] zlibbioc_1.30.0 rlang_0.4.0
## [13] lazyeval_0.2.2 jquerylib_0.1.4
## [15] Matrix_1.2-17 rmarkdown_2.11
## [17] labeling_0.3 BiocParallel_1.18.1
## [19] stringr_1.4.0 RCurl_1.95-4.12
## [21] munsell_0.5.0 DelayedArray_0.10.0
## [23] compiler_3.6.1 xfun_0.29
## [25] pkgconfig_2.0.2 htmltools_0.3.6
## [27] tidyselect_0.2.5 SummarizedExperiment_1.14.1
## [29] tibble_2.1.3 GenomeInfoDbData_1.2.1
## [31] XML_3.98-1.20 crayon_1.3.4
## [33] withr_2.1.2 GenomicAlignments_1.20.1
## [35] bitops_1.0-6 grid_3.6.1
## [37] gtable_0.3.0 lifecycle_0.1.0
## [39] stringi_1.4.3 ellipsis_0.2.0.1
## [41] vctrs_0.2.0 tools_3.6.1
## [43] Biobase_2.44.0 glue_1.3.1
## [45] purrr_0.3.2 colorspace_1.4-1
## [47] caTools_1.17.1.2 knitr_1.24